metafor: Meta-Analysis Package for R, version 1.9-3. This product consists of an updated, new version of this software for conducting phylogenetic mixed meta-analysis models using likelihood methods. One of our working group members, Dr. Wolfgang Viechtbauer, responded to our group needs (and the needs of the broader scientific community) by adding the capability of fitting arbitrary random effects and one or more phylogenies in his meta-analysis package in R, metafor. This package was already the most powerful in R for meta-analysis with maximum likelihood model fitting, and now has significantly broader applicability to a wide range of model structures. Working group members provided significant feedback about the desired capabilities in this package, and Dr. Viechtbauer has since completed an official release of the new version of the package. New is the rma.mv function, which allows specification of an arbitrary number of random effects, and known correlation matrices. This new version was released on 5/5/2014.

CodonAlign: Codon alignment and analysis in Biopython. Ruan, Z., Talevich, E., & Cock, P. 2013. CodonAlign: Codon alignment and analysis in Biopython. The CodonAlign (Bio.CodonAlign) module extends biopython to support estimations of nonsynonymous substitutions per site (dN) and synonymous substitutions per site (dS), and neutrality testing. CodonAlign currently support three counting based methods (NG86, LWL85, YN00) and maximum likelihood method to estimate dN and dS. Project specific code is available at: https://github.com/zruan/biopython/tree/master/Bio/CodonAlign.

Extending PartitionFinder to automatically partition DNA and protein alignments. Frandsen, P. Lanfear, R., & Calcott, B. 2013. Extending PartitionFinder to automatically partition DNA and protein alignments. Implements a new algorithm that uses site rates or site likelihoods to automatically partition sites in DNA and protein alignments into a best fit partitioning scheme. PartitionFinder can be downloaded from: http://www.robertlanfear.com/partitionfinder/ or github.

GeneValidator: Identify problems with gene predictions. Dragan, M., Priyam, A., & Wurm, Y. 2013. GeneValidator: Identify problems with gene predictions. GeneValidator identifies problems with gene predictions and provides information based on the similarities to genes in public databases. Results of prediction validation can inform sequencing curation and improvement of approaches and tools for gene prediction. GeneValidator was designed for use by biologists who want to validate data obtained in their own laboratories.

Implementing Machine Learning Algorithms for Classification and Feature Selection in mothur. Lynch, J., Iverson, K., Zaher Md. Faridee, A. 2013. Implementing machine learning algorithms for classification and feature selection in mothur. Extended mothur through implementation of the support vector machine algorithm to support a new classification and feature selection command in mothur. Project-specific code is available at https://github.com/jklynch/mothur; mothur can be downloaded from http://www.mothur.org/ and github.

owlet. Owlet is a query expansion preprocessor for SPARQL. It parses embedded OWL class expressions (in Manchester Syntax) and uses an OWL reasoner to replace them with FILTER statements containing the URIs of subclasses of the given class expression (or superclasses, equivalent classes, or instances).

Phylet: Open Tree of Life Graph Visualization and Navigation. Phelan, C., Harp, G., & Smith, S.A. 2013. Phylet: Open Tree of Life graph visualization and navigation. Phylet is a visualization tool for phylogenetic graphs, powered by the graph database Neo4j and visualized by the JavaScript library D3. Hierarchical (rather than network) graphs are used to represent tree structures. In addition to other types of relationships, conflicts are also displayed. This application can be used by specialists and general lay audiences.

Phylogenetics in Biopython: Filling in the gaps. Ye, Yanbo; Holder, Mark; Sukumaran, Jeet; Talevich, Eric. 2013. Phylogenetics in Biopython: Filling in the gaps. TreeConstruction and Consensus modules for Bio.Phylo were constructed to extend biopython support for tree construction and consensus tree algorithms. These modules add UPGMA, NJ, MP, strict consensus, majority rule, adam consensus with some branch support, and bootstrap algorithms to the current package.

scowl. Scowl is a Scala library allowing a declarative approach to composing OWL expressions and axioms using the OWL API.

Species Autocomplete. Vaidya, G. 2013. Species Autocomplete. This tool provides basic Javascript and PHP code to run an autocompletion script. An included Perl script allows the ITIS-DwCA resource to be used to generate the autocompletion database (in SQLite). Further improvements may allow this software program to be integrated into websites which would like to validate the input of scientific names, either for data entry or to power searches.

vue2owl. A tool for converting a VUE diagram document to an OWL ontology.

ITIS-DwCA. The TNRS group contacted David Mitchell, ITIS Data Specialist at the NMNH, who gave us permission to make the entire ITIS database available as a DarwinCore Archive. This file was generated by dwca-hunter (https://github.com/GlobalNamesArchitecture/dwca-hunter), a Ruby program developed by the Global Names Architecture. I wrote a small script to automatically organize dwca-hunter's results, and have been running it regularly and uploading the results to http://gaurav.github.com/itis-dwca/.

jMatrixBrowse: Coordinate-based browsing for matrices. Goyal, P. & Baron, C. 2012. jMatrixBrowse: Coordinate-based browsing for matrices. jQuery plugin for browsing large matrices using dragging (like Google Maps). The main features of the tool include a browsable canvas that can be panned and zoomed easily.

MASTodon: Summary and visualization of phylogenetic tree sets. Zarins, J., Rambaut, A., Cranston, K., Redelings, B. 2012. MASTodon: Summary and visualization of phylogenetic tree sets. MASTodon looks for a common subtree in a large set of phylogenetic trees. Suitability of a subtree is measured with a MAP (maximum a-posteriori probability) score. MASTodon prunes some taxa from all trees and compares each against the MAP tree. This is the same as counting the trees that contain the subtree that is obtained if you remove the selected taxa from the trees. Command line and graphical interfaces are provided. Several pruning algorithms are available, and it is possible to add more.

Mesquite-o-tastic - a Mesquite package for retrieving trees from Phylotastic. Midford, P. E. 2012. Mesquite-o-tastic - a Mesquite package for retrieving trees from Phylotastic. This is a prototype package that allows a user to retrieve a tree from phylotastic that matches the taxa present in a Mesquite character matrix. See the demo video by Arlin Stoltzfus at
http://www.youtube.com/watch?v=Lak-zjwFuhQ&feature=youtube_gdata_player

Newick to CDAO Ingestor. The Newick to CDAO ingestor is a Perl module. The module takes as input a tree described in Newick format and produces a CDAO representation of the tree.
The module is capable of contacting the Phylotastic TNRS to resolve names and adds the result of the name resolution to the CDAO representation of the tree.

obo-lint. Plugin for the Protege ontology editing environment which displays axioms which can not be represented in an OBO format serialization of the ontology.

Ontology and RDF model for Taxonomic Name Resolution Service results. . Lapp H. 2012. Ontology and RDF model for Taxonomic Name Resolution Service (TNRS) results. The ontology describes the entities that make up a TNRS result and the relationship between those and those between an OTU and a TNRS resolution result. The RDF model is accompanied by an instance document and a graph visualization.

OpenSim grid hosting on Amazon's EC2.. Using the OpenSim software, a 6 region grid was set up on virtual machine instances at Amazon's EC2 to host the 3D environments for this project. The EC2 API tools were used to automate starting and stopping the server instances in order to reduce costs by not running the instances at night when they are not used. Monitoring software was set up to restart the OpenSim software in case of errors.

Phenex 1.2. New release of the Phenex annotation software with new features supporting collaborative editing across file sharing systems such as Dropbox.

Phylogeny pruner based on MapReduce with web page and services interface. Rutger Vos, 2012. A phylotastic pruning service based on MapReduce. HIP working group of NESCent.
This pruner was developed to provide automated pruning services, as part of the Phylotastic project. Given a set { S } of OTU names, and the name of a source tree, the pruner returns a topology for the OTUs that it can match from { S }. This kind of pruning can be done by recursive calls into a database (which probably would need to hit the database many times) or by loading the whole tree into memory (which might take a while to read in the file, and cost a bit of memory). The way it is done here is much cooler, because it never requires the whole tree to be in memory or in a database: the pruning is done in parallel using MapReduce. Some tests on the entire dump of the Tree of Life Web Project showed that this returns a pruned subtree within a few seconds, fast enough for a web service. The pruner has two interfaces, a web forms interface (with explanatory text and examples) and a web-services interface. The code and some documentation is available at a location indicated on the web page.

Phylomatic v3. A major upgrade to this well-used tool. Phylomatic version 3 is a fork of the phylocom phylomatic code and exists only as a web service. I can now: read in trees as NeXML and CDAO, graft in taxa to the megatree, and write out in a number of formats.

PhyloTastic services in Galaxy. To provide end-users with a familiar graphical user interface with which to access PhyloTastic services I have developed several wrapper classes that enable interaction with TNRS, DateLife, BabelPhysh and pruning functionality within the Galaxy web application. A demo Galaxy instance is available at http://galaxy.phylotastic.org, the source code at https://github.com/phylotastic/arch-galaxy and a screen cast that demonstrates the currently available functionality is available at http://youtu.be/kMME658xOu4

prototype controller as Perl CGI script . The Perl controller coordinates stub CGI implementations of the Phylotastic TNRS, tree store, topology, and branch length services which produce correct output for one example input. However, the user may substitute real service implementations into the controller workflow via CGI parameters, allowing the services to be tested for conformance to the Phylotastic specification. Usage instructions for the CGI controller, along with example input/output files for the stub services, are provided at https://github.com/phylotastic/cgi.

Reconciliotastic. Reconcili-o-tastic starts with a gene tree, discovers the species sources, gets a tree for the species on the fly (phylotastically), then runs reconciliation software to identify which branchings represent speciations vs duplications.

Taxonomy Ontology Tool (VTOTool). Midford, P. E. 2012. Taxonomy Ontology Tool (VTOTool). This tool constructs taxonomic ontologies (e.g., Phenoscape's VTO) from multiple taxonomic sources - existing ontologies (e.g., TTO) as well as other taxonomic sources (e.g., NCBI, CoL, PBDB). As of July 2012 it generates the ontologies in an OBO format where taxonomic groups are classes and follows the conventions of the OBO rendering of the full NCBI taxonomic ontology. A earlier version of this tool was used in support of a working group.

Taxosaurus: A Phylotastic Taxonomic Name Resolution Service. Taxosaurus is a meta TNRS that implements the TNRastic API. It's composed by 2 main modules (the handler_library and the processor) that sit behind an http handler. The handler_library implements the TNRastic API whereas the processor coordinates the execution of the downstream calls to the sources.
The processor itself has a modular design that allows the addition of new service via adaptors that are registered through a simple JSON description.

TNRastic API. The TNRastic API is a lightweight RESTful API specification that provides a generalized framework to access Taxonomic Name Resolution Services. It's composed of a set of services that are essential for name resolution.

Tools to convert trees of Goloboff, et al. (2009) from TNT to Newick format. The phylogeny from Goloboff, et al. "Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups" (Cladistics 2009, 25:211-230) is a valuable resource, useful for the Phylotastic project. However, it is available only in TNT format, a nested-parenthesis format like Newick. The tree file has only numeric codes, with names encoded in a separate file. Converting this information into a single Newick tree is a 3-step process:
1. convert the TNT trees (in any of the *.tre files) to newick
2. pick the tree you want and put it in a file by itself
3. replace the numeric codes in the tree with species names from Taxon_Names_Only.tnt
I developed and tested Perl scripts for steps 1 and 3. The scripts contain documentation using POD. They are available from a public repository using the URL below.

Towards a fully RNA-aware alignment editor with Jalview and VARNA. Menard, A., Ponty, Y., & Procter, J. Towards a fully RNA-aware alignment editor with Jalview and VARNA. This project focused on the synchronization of Jalview and VARNA to improve jalview RNA support, with emphasis on tertiary interactions. Tertiary interactions can now be loaded from XML files (RNAML format), directly annotated from 3D experimental models (PDB files), and displayed graphically using an integrated version of the Varna software.

Enhancing phyloGeoRef. Verma, A., & Iverson, K.D. 2011. PhyloGeoRef.
Java library that takes a phylogenetic tree and metadata associated with taxonomic units in the tree as input; and creates a kml file that can be viewed in Google Earth. This project focused on enhancing phyloGeoRef through the addition of a GUI for non-Java users; and weighted means for node positioning.

API for NeXML I/O and RDF triples for BioRuby . Priyam, A., Vos, R., & Aerts, J. 2010. BioRuby API for NeXML I/O and RDF triples.
Adds support to work with RDF and NeXML in BioRuby; and provides methods to semantically annotate and query BioRuby objects.

BAli-Phy version 2.1.0. (Released 7/7/2010) BAli-Phy is a Bayesian MCMC program for estimating phylogenies and sequence alignments jointly from unaligned sequence data.
BAli-Phy can estimate phylogenies without bias toward a guide tree, when the alignment is uncertain.

Phenoscape Ontologies. Wasila Dahdul and Peter Midford. 2010. Phenoscape Ontologies. Phenoscape is using multiple ontologies to describe variation in phenotypes across species. We have developed several new ontologies required for evolutionary biology, including the Teleost Anatomy Ontology (TAO) and the Teleost Taxonomy Ontology (TTO). As community resources, these ontologies are available within the OBO Foundry . Wasila Dahdul and Peter Midford are the maintainers of the ontologies developed by Phenoscape.

TreeBASE. TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) representing all biotic taxa. A second-generation version of TreeBASE was released in 2010 and is hosted by NESCent.
Source code: http://sf.net/projects/treebase

beagle-lib: A general purpose library for evaluating the likelihood of sequence evolution on trees. Alexei Drummond. 2009. A project to create an open API and fast implementations of a library for evaluating phylogenetic likelihoods (continuous time Markov processes) of biomolecular sequence evolution. The aim is to provide high performance evaluation 'services' to a wide range of phylogenetic software, both Bayesian samplers and Maximum Likelihood optimizers. This will allow these packages to make use of implementations that make use of optimized hardware such as graphics processing units.

BioLib mapping for the libsequence population genetic libraries. Shuai, X., Fields, C., Prins, P. 2009. BioLib mapping for the libsequence population genetic libraries. Extends the BioLib project by adding access to Libsequence, a C++ library for population genetic simulation and the evolutionary analysis of molecular data. Mappings to Perl and Python made available using SWIG.

Build a Mesquite package to view Phenex-generated Nexml files. Hayden, K., Midford, P., Balhoff, J. 2009. 'Build a Mesquite package to view Phenex-generated Nexml files', a Google summer of code project. This project resulted in a Mesquite plug-in package that used the nexml library for java to parse and display ontology-based annotations from nexml files generated by Phenex. The tool displays annotations within the Mesquite character matrix editor.

Dryad. Todd Vision, Ryan Scherle, Hilmar Lapp, Jane Greenberg, Peggy Schaeffer, Kevin Clarke, Peter Midford, Mark Diggory. 2012. Dryad - a repository of data underlying scientific publications, with an initial focus on evolutionary biology and related fields. Developed by Nescent and the University of North Carolina Metadata Research Center, in coordination with a large group of Journals and Societies in evolutionary biology and ecology.Source code: http://dryad.googlecode.com/

PHLAWD: phylogenetic dataset construction. Smith, S.A. (2009). PHLAWD: phylogenetic dataset construction. PHLAWD (pronounced flawd) allows for the rapid creation of large (mega) phylogenies using NCBI databases. PHLAWD takes advantage of multi threaded computers and can produce matrices of more than 100,000 taxa. Target audiences for PHLAWD include evolutionary biologists hoping to mine GenBank for data associated with their lineages, and also
comparative biologists and ecologists who want to develop phylogenetic hypotheses. Binaries for MacOSX and Linux are available at: http://code.google.com/p/phlawd. It is recommended that you work with the source code for the most updated version (https://github.com/blackrim/phlawd). The manual is at the PHLAWD site: http://phlawd.net/.

phyloXML support in BioRuby. Jaunzeikare, D. & Zmasek, C. 2009. phyloXML support in BioRuby. 2009. Reading and writing capabilities for phyloXML in BioRuby.

Phylr. Participants of the Evolutionary Database Interoperability Hackathon. 2009. Phylr is an initial proof-of concept implementation of the PhyloWS API, making phylogenetic information available via a standard set of web services.

Publication of GBIF Data via SADI Semantic Web Services. Extension of the SADI (Semantic Automated Discovery and Integration) system to integrate biodiversity data. A demo SADI Web Service was created showing how GBIF (http://vocabularies.gbif.org/) data can be served via SADI (Semantic Automated Discovery and Integration). A second service was constructed that extracts taxonomy information from the UniProt protein record.

VertNet: global museum database of vertebrate natural history collections. Constable, H and Russell, L. 2009. VertNet is a global museum database of vertebrate natural history collections. Four distributed database networks (MaNIS, HerpNET, ORNIS and FishNet) have been the result of a massive, collaborative effort within the museum and bioinformatics communities to make specimen data interoperable, mappable and publicly available. VertNet was formed as an umbrella project to meet the common needs of the participants, maintain the existing networks, add new members and develop integrated online technologies.

Brownie. O'Meara, B.C. 2008. Brownie 2.1. Brownie is a program for analyzing rates of continuous character evolution and looking for substantial rate differences in different parts of a tree using likelihood ratio tests and Akaike Information Criterion (AIC) statistics. It now also implements many other methods for examining trait evolution and methods for doing species delimitation. See below for info on downloading the program. http://www.brianomeara.info/brownie

Dupertree. Wehe, A., M.S. Bansal, J.G. Burleigh, and O. Eulenstein. 2008. Dupertree: a program for large-scale gene tree parsimony phylogenetic analyses. Dupertree describes a new program for inferring phylogenies by gene tree parsimony. It is also publicly available. Other software used to build supertrees and identify ancient large-scale duplication events in the above manuscripts will eventually be released to the public.

Enhancing the representation of ecophylogenetic tools in R Picante. Helmus, M., Kembel, S., Bolker, B. 2008. Enhancing the representation of ecophylogenetic tools in R Picante. Added methods to assess phylogenetic community structure; the effects of environmental variables on phylogenetic community structure; and phylogenetic structure among species interactions in the R package Picante.

Matrix display of phenotype annotations using ontologies in Phenote. Wallinga, M., & Balhoff, J. 2008. Matrix display of phenotype annotations using ontologies in Phenote. Extends Phenote by adding matrix representations of annotation data. The matrix is populated by consolidating phenotype annotations into characters by finding values which descend from the same attribute within the PATO phenotype ontology; and character values are grouped by taxon and character.

MIAPA annotation tool. Stoltzfus, A. 2008. MIAPA annotation tool (proof-of-concept software). To demonstrate the potential for users to construct their own ontology-based MIAPA annotations, as in the knowledge capture experiment below, we have created a proof-of-concept application by adapting Phenote. The result is an interactive graphical tool for user-generated, ontology-bound MIAPA annotations.

Phenex. Jim Balhoff. 2008. Phenex - an application for annotating character matrix files with ontology terms. Character states can be annotated using the Entity-Quality syntax for ontologically describing phenotypes. In addition, taxon entries can be annotated with identifiers from a taxonomy ontology. Phenex saves ontology annotations alongside traditional character matrix data using the new NeXML format standard for evolutionary data

Phenoscape Website (http://phenoscape.org). Public interface for the Phenoscape Project. Phenoscape was initiated to create a scalable infrastructure that enables linking descriptive phenotype observations across different fields of biology by the semantic similarity of their free-text descriptions.

PhyloFinder. Chen, D., J.G. Burleigh, M.S. Bansal, and D. Fernandez-Baca. 2008. PhyloFinder: an intelligent search engine for phylogenetic tree databases. BMC Evol. Biology 8:90. describes a new software tool for accessing data from tree databases.
The software home page at http://pilin.cs.iastate.edu/phylofinder/ has become unavailable, and no other location is known.

Primate Life Histories Database. Hilmar Lapp, Xianhua Liu, members of the Primate Life Histories Working Group. Primate Life Histories Database. Code at http://github.com/NESCent/plhdb , online application at http://plhdb.org

SAX based phyloXML support in BioPerl. Han, M., Fields, C. 2008. SAX-based phyloXML support in BioPerl. Extends BioPerl by adding a parser to read and write phyloXML; also enabled addition of general annotations in the BioPerl Node module.

Tree and data plotting in phylobase. Cowan, P., & Bolker, B. 2008. Tree and data plotting in the phylobase project. Implements a plotting function for visualizing phylo4 and phylo4d data objects. A key feature of the functions is the use of the grid graphics interface. This interface allows more flexible plot resizing and pushing of arbitrary plots to tree tips.

TreEvo. O'Meara, B.C. 2008. TreEvo. TreEvo (TREE + EVOlution) is an assortment of methods for understanding evolution using trees. It aims to be compatible and complementary with the wide assortment of existing packages in this area in R.

BioPrio. Klaas Hartmann, Tobias Thierer, Rutger Vos. 2007. BioPrio. BioPrio implements various algorithms that utilize phylogenetic information to prioritize species for biodiversity conservation and provides a GUI that allows these to be utilized by conservation managers.

Extending Geiger with fitContinuous and fitDiscrete. Harmon, L., Hipp, A., & Hunt. (2007). Extending Geiger with fitCountinuous and fitDiscrete. NESCent Hackathon on Comparative Methods in R, Trait Evolution Subgroup, 10-14 December, 2007. Geiger was modified to give more reliable results by a more thorough search of the likelihood surface (fitContinuous) and to deal with a more general set of discrete character models (fitDiscrete). Geiger's tree transformations improved to work for nonultrametric trees.

GARLI. Derrick Zwickl and James Balhoff. 2007. GARLI (Genetic Algorithm for Rapid Likelihood Inference) performs phylogenetic searches on aligned sequence datasets using the maximum-likelihood criterion. Version 0.96 is a major revision from the previous version 0.951. It includes many new features, including the ability to perform tree inference using amino acid and codon-based models, in addition to the standard nucleotide-based models available in previous versions. On a practical level, the program is able to perform maximum-likelihood tree searches on large datasets in a number of hours.

GeoPhylobuilder. David Kidd and Xianhua Liu. 2007. GeoPhylobuilder is an ESRI ArcGIS extension that creates a spatial network, a geophylogeny, from a tree file and associated geographical data.

NeXML. Rutger Vos, Jason Caravas and participants of the EvoInformatics working group. 2007. NeXML is an exchange standard for representing phylogenetic data inspired by the commonly used NEXUS format, but more robust and easier to process.

PhyloGeoViz. Yi-Hsin Tsai and David Kidd. 2007. PhyloGeoViz is a web based application that generates geographic maps (using the Google Maps API) of DNA haplotype data that are often used in the course of phylogeographic analysis.

PhyloWidget. Gregory Jordan and William Piel. 2007. PhyloWidget is a user-friendly and web-embeddable GUI based on Java/Processing for creating, navigating, and manipulating phylogenetic trees.

Prototype Database of Mixed Mating System . Susan Kalisz, Mark Johnston and members of the Mixed Mating Working Group. 2007. The prototype database integrates comprises four separate databases. 1) The mating system database contains information on estimates of selfing/outcrossing rate and/or the inbreeding coefficient measured at the population level for 475 species. 2) The inbreeding depression database contains information on estimates inbreeding depression measured across the life history (3-stage or 4-stage IBD) measured at the population level. 3) The experimental pollination database contains information at the population level on experimental tests of selfing, outcrossing, pollen limitation, reproductive assurance, timing of selfing, etc. 4) The species traits database contains data on the average morphological, phenological, life history and habitat characteristics for all 475 species in the mating system database. Significantly, all four databases contain citations to the original publications from which the data were extracted.

Summary data on local adaptation, species traits, and experimental design across 29 cross-inoculation studies of species interactions. Hoeksema J. D. and S. Forde. 2007. Summary data on local adaptation, species traits, and experimental design across 29 cross-inoculation studies of species interactions.

xrateparser. Leung, J., & Lewis, S. xrateparser. A Perl module that runs as a web application to harnesses xrate for tree generation as .png or .svg images. Trees are generated from raw .tre files (Newick format) of .stk files, and are .png or .svg images of trees to be displayed on a webpage.

xREI. Lars Barquist and Ian Holmes. 2007. xREI is an AJAX-based web interface and visualization server for xrate and its grammar files.

PhyloDB. Hilmar Lapp and William Piel. 2006. The PhyloDB module extends the core BioSQL schema to allow storing phylogenetic trees or reticulate networks and metadata in a simple yet extensible way. An associated Perl script loads the ITIS taxonomy into the module.